rs9528094

Variant names:

• chr13-60274914-C-T
• rs9528094
• ENST00000448913.1:n.139C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000448913.1(TARDBPP2):​n.139C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.531 in 1,411,864 control chromosomes in the GnomAD database, including 201,653 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.49 (18729 hom., cov: 32)
  • Exomes 𝑓: 0.54 (182924 hom.)
• Consequence: TARDBPP2 ENST00000448913.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.15
• Publications: 7 publications found

Genes affected

TARDBPP2 (HGNC:39848): (TARDBP pseudogene 2)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000448913.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TARDBPP2	ENST00000448913.1	TSL:6	n.139C>T		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74586 AN: 151826 Hom.: 18711 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.444

GnomAD4 exome AF: 0.536 AC: 675731 AN: 1259920 Hom.: 182924 Cov.: 22 AF XY: 0.536 AC XY: 339846 AN XY: 634050

African (AFR) AF: 0.378 AC: 11184 AN: 29588

American (AMR) AF: 0.475 AC: 20298 AN: 42718

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 9645 AN: 24416

East Asian (EAS) AF: 0.582 AC: 22257 AN: 38242

South Asian (SAS) AF: 0.550 AC: 44453 AN: 80876

European-Finnish (FIN) AF: 0.550 AC: 28376 AN: 51592

Middle Eastern (MID) AF: 0.383 AC: 2043 AN: 5330

European-Non Finnish (NFE) AF: 0.547 AC: 510707 AN: 934070

Other (OTH) AF: 0.504 AC: 26768 AN: 53088

GnomAD4 genome AF: 0.491 AC: 74654 AN: 151944 Hom.: 18729 Cov.: 32 AF XY: 0.493 AC XY: 36619 AN XY: 74254

African (AFR) AF: 0.396 AC: 16395 AN: 41442

American (AMR) AF: 0.459 AC: 7009 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1394 AN: 3470

East Asian (EAS) AF: 0.545 AC: 2800 AN: 5142

South Asian (SAS) AF: 0.543 AC: 2614 AN: 4814

European-Finnish (FIN) AF: 0.553 AC: 5839 AN: 10552

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.547 AC: 37142 AN: 67942

Other (OTH) AF: 0.444 AC: 937 AN: 2110

Alfa AF: 0.522 Hom.: 86093

Bravo AF: 0.478

Asia WGS AF: 0.464 AC: 1616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	8.3
DANN	Benign	0.73
PhyloP100		5.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9528094;

hg19: chr13-60849048;